Learning and exploring Life science through the EBI reosurces and tools BIOQUEST workshop_2011 Vicky Schneider, EMBL-EBI Training Programme Project leader

Services

3 Principles of service provision Comprehensive Compatibility PortabilityQuality Patrick Hoesly

4 Databases: molecules to systems Genomes Ensembl Ensembl Genomes EGA Genomes Ensembl Ensembl Genomes EGA Nucleotide sequence ENA Nucleotide sequence ENA Functional genomics ArrayExpress Expression Atlas Functional genomics ArrayExpress Expression Atlas Protein Sequences UniProt Protein Sequences UniProt Protein families, motifs and domains InterPro Protein families, motifs and domains InterPro Macromolecular PDBe Macromolecular PDBe Protein activity IntAct, PRIDE Protein activity IntAct, PRIDE Chemical entities ChEBI Chemical entities ChEBI Pathways Reactome Pathways Reactome Systems BioModels BioSamples Systems BioModels BioSamples Literature and ontologies CiteXplore, GO Literature and ontologies CiteXplore, GO Chemogenomics ChEMBL Chemogenomics ChEMBL

5 Database collaborations

6 Standards development – international collaborations Genome annotation Genome annotation Functional Genomics Data Society Protein sequence Protein sequence HUPO- Proteomics Standards Initiative (PSI) HUPO- Proteomics Standards Initiative (PSI) Protein structure Protein structure Cheminformatics Cheminformatics Pathways Pathways Systems modelling standards Systems modelling standards Metabolomics Standards Initiative (MSI) Metabolomics Standards Initiative (MSI) Genomics Standards Consortium (GSC) Genomics Standards Consortium (GSC) Nucleotide sequence Nucleotide sequence

New search service Access from the EBI’s homepage Data organised according to: gene expression protein structure literature Data organised according to: gene expression protein structure literature Species selector allows for easy comparison Explore data, return easily to your results Explore data, return easily to your results 7

Goals of the new EBI Search Relevant to ‘wet-lab’ biologists Organises information based around a single gene (or a small number of genes) User-expectation centric (not database centric) Smooth transition to the detailed information in many of EBI’s core databases NOT for bioinformaticians: does not provide programmatic access 8

Quick databases tour 9

10 Genomes 1: Ensembl Synteny Pick a genome Gene trees Genomic alignments Gene families Variations Genes Chromosomes User Upload Variation Effect Predictor

11 Genomes 2: Ensembl Genomes Interface uses Ensembl technology Pan-taxonomic comparative analysis Genome portals for the five kingdoms of life Multi-way comparison of whole bacterial chromosomes Variation data for plant, metazoan and fungal species

12 Nucleotides: European Nucleotide Archive (ENA) Figure adapted from: Cochrane, G. et al. Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure. In: Metagenomics: Theory, Methods and Applications (Chapter 5), Caister Academic Press, Universidad Nacional de Cordoba, Argentina. Ed. D. Marco (2010). The ENA has a three-tiered data architecture. It consolidates information from EMBL-Bank, the European Trace Archive (containing raw data from electrophoresis-based sequencing machines) and the Sequence Read Archive (containing raw data from next-generation sequencing platforms).

13 Transcriptomes: ArrayExpress Expand results Search by keyword ArrayExpress Archive: browse experiments Spreadsheets describing the sample properties

Transcriptomes : Gene Expression Atlas Search by gene or biological condition Gene page Atlas: browse changes in gene expression Experiment page 14

15 Input sources for UniProtKB UniProt Manual curation Literature-based annotation Sequence analysis Automated annotation PRIDE GO InterPro IntAct IntEnz HAMAP RESID Functional info Protein identification data Protein families and domains Molecular interactions Enzymes Microbial protein families Post-translational modifications Some data sources for annotation Transmembrane prediction InterPro classification Signal prediction Other predictions Protein classification

16 Protein families, motifs and domains: InterPro Powerful tool for protein classification, integrating several methods into one resource View architectures of proteins containing a signature Compare methods of protein signature prediction Visualise the taxonomic range for a protein signature

17 Proteomics services IntAct: molecular interactions INTENZ: enzyme classification ChEBI: small molecules PRIDE: protein identifications from proteomics experiments

18 Structures: PDBe

Chemical entities: ChEBI 19 Link to other databases View mappings to other databases View structure, nomenclature, formula and more View relationships in the ChEBI Ontology Download flat files, database dumps and the ChEBI Ontology for local installation

Chemogenomics: ChEMBL 20 ChEMBL Neglected Tropical Disease (NTD) archive ChEMBL database Browse targets Target search Search results Compound search Kinase SARfari GPCR SARfari

21 Pathways: Reactome Export pathway to your favourite modelling software Compare events in different species Link to source databases View expression values overlaid on a pathway Interaction overlay on a pathway diagram

22 Data management Leased two new data centres (with €11.4M from UK Research Councils) Over 800 million cross- references in the databases we serve Over 4M web requests per day – over 4.6M if Ensembl is included Over 280,000 unique hosts served per month, excluding Ensembl Total disk space: 10 petabytes in 2010.

23 User support support – Online help pages – 2Can bioinformatics user support – eLearning Portal – coming soon